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Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank

BACKGROUND: Glycans are involved in a wide range of biological process, and they play an essential role in functions such as cell differentiation, cell adhesion, pathogen-host recognition, toxin-receptor interactions, signal transduction, cancer metastasis, and immune responses. Elucidating pathways...

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Detalles Bibliográficos
Autores principales: Hashimoto, Ryo, Hirose, Kazuko, Sato, Taku, Fukushima, Nobuhiro, Miura, Nobuaki, Nishimura, Shin-Ichiro
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907334/
https://www.ncbi.nlm.nih.gov/pubmed/20584338
http://dx.doi.org/10.1186/1752-0509-4-91
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author Hashimoto, Ryo
Hirose, Kazuko
Sato, Taku
Fukushima, Nobuhiro
Miura, Nobuaki
Nishimura, Shin-Ichiro
author_facet Hashimoto, Ryo
Hirose, Kazuko
Sato, Taku
Fukushima, Nobuhiro
Miura, Nobuaki
Nishimura, Shin-Ichiro
author_sort Hashimoto, Ryo
collection PubMed
description BACKGROUND: Glycans are involved in a wide range of biological process, and they play an essential role in functions such as cell differentiation, cell adhesion, pathogen-host recognition, toxin-receptor interactions, signal transduction, cancer metastasis, and immune responses. Elucidating pathways related to post-translational modifications (PTMs) such as glycosylation are of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids and various biological events are considered extremely valuable and convenient tools for the systematic investigation of PTMs. However, there is no database which dynamically draws functional networks related to glycans. DESCRIPTION: We have created a database called Glyco-Net http://www.glycoconjugate.jp/functions/, with many binary relationships among glycan-related molecules. Using search results, we can dynamically draw figures of the functional relationships among these components with nodes and arrows. A certain molecule or event corresponds to a node in the network figures, and the relationship between the molecule and the event are indicated by arrows. Since all components are treated equally, an arrow is also a node. CONCLUSIONS: In this paper, we describe our new database, Glyco-Net, which is the first database to dynamically show networks of the functional profiles of glycan related molecules. The graphical networks will assist in the understanding of the role of the PTMs. In addition, since various kinds of bio-objects such as genes, proteins, and inhibitors are equally treated in Glyco-Net, we can obtain a large amount of information on the PTMs.
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spelling pubmed-29073342010-07-21 Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank Hashimoto, Ryo Hirose, Kazuko Sato, Taku Fukushima, Nobuhiro Miura, Nobuaki Nishimura, Shin-Ichiro BMC Syst Biol Database BACKGROUND: Glycans are involved in a wide range of biological process, and they play an essential role in functions such as cell differentiation, cell adhesion, pathogen-host recognition, toxin-receptor interactions, signal transduction, cancer metastasis, and immune responses. Elucidating pathways related to post-translational modifications (PTMs) such as glycosylation are of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids and various biological events are considered extremely valuable and convenient tools for the systematic investigation of PTMs. However, there is no database which dynamically draws functional networks related to glycans. DESCRIPTION: We have created a database called Glyco-Net http://www.glycoconjugate.jp/functions/, with many binary relationships among glycan-related molecules. Using search results, we can dynamically draw figures of the functional relationships among these components with nodes and arrows. A certain molecule or event corresponds to a node in the network figures, and the relationship between the molecule and the event are indicated by arrows. Since all components are treated equally, an arrow is also a node. CONCLUSIONS: In this paper, we describe our new database, Glyco-Net, which is the first database to dynamically show networks of the functional profiles of glycan related molecules. The graphical networks will assist in the understanding of the role of the PTMs. In addition, since various kinds of bio-objects such as genes, proteins, and inhibitors are equally treated in Glyco-Net, we can obtain a large amount of information on the PTMs. BioMed Central 2010-06-29 /pmc/articles/PMC2907334/ /pubmed/20584338 http://dx.doi.org/10.1186/1752-0509-4-91 Text en Copyright ©2010 Hashimoto et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database
Hashimoto, Ryo
Hirose, Kazuko
Sato, Taku
Fukushima, Nobuhiro
Miura, Nobuaki
Nishimura, Shin-Ichiro
Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title_full Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title_fullStr Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title_full_unstemmed Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title_short Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank
title_sort functional network of glycan-related molecules: glyco-net in glycoconjugate data bank
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907334/
https://www.ncbi.nlm.nih.gov/pubmed/20584338
http://dx.doi.org/10.1186/1752-0509-4-91
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